## Software

# FIT2D

FIT2D is a general purpose 1 and 2 dimensional data analysis program. It is used for both interactive and "batch" data processing, and is used for different purposes. Calibration and correction of detector distortions is one of the main uses of FIT2D. Difficult data analysis problems may be tackled using fitting of user specified models. To enable model fitting to be performed on a wide variety of input data, many other more basic data analysis operations are also available. A wide variety of performant graphical display methods are available.

# FLUKA

FLUKA is a fully integrated particle physics MonteCarlo simulation package from CERN and INFN. It has many applications in high energy experimental physics and engineering, shielding, detector and telescope design, cosmic ray studies, dosimetry, medical physics and radio-biology. It is used for radiation shielding simulations in the safety group.

# Fox/ObjCryst++

The FOX program was made for ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Its most interesting features for ab initio structure determination are: * a versatile description of the crystal contents: either isolated atoms , molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions.. * an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms. * the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern) * smart global optimization algorithms which can get out of false minima. * a graphical interface (see the screenshots) with a 3D crystal structure view, with live updates during the optimization process.

# freeart

ART algorithms for fluorescence and transmission tomography reconstructions. Fluorescence absorption for the incoming and outgoing beams are taken into account.

# Frida

Frida (“Fast reliable interactive data analysis”) is a versatile data analysis program with special routines for inelastic neutron scattering.

# GATE

GATE is an opensource software package developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), Computed Tomography (CT), Optical Imaging (Bioluminescence and Fluorescence) and Radiotherapy experiments.

# GDFIDL

GdfidL computes electromagnetic Fields in 3D-Structures using parallel or scalar Computer Systems. GdfidL computes Resonant Fields in lossfree or lossy Structures and Time dependent Fields in lossfree or lossy Structures. The Fields may be excited by Port Modes or relativistic Line Charges. The Postprocessor computes from these Fields eg. Scattering Parameters, Wake Potentials, Q-Values and Shunt Impedances.

# GEANT4

Toolkit for the simulation of the passage of particles through matter. Main applications: high energy, nuclear and accelerator physics, as well as studies in medical and space science.

# GENFIT (and SASMOL)

GENFIT is a software tool for analysing small-angle scattering (SAS) data from X-ray (SAXS) or neutron (SANS) experiments. It reads in a set of one-dimensional scattering curves and fits them using different kinds of models. SAS curves calculated from a model can be smeared to allow for the instrumental resolution. The user can fit the experimental data selecting one or more models from a list including more than 30 models, starting from simple asymptotic behaviours (Guinier's law, Porod's law, etc.) down to complete atomic structures. Some models, which are defined in terms of both form and structure factors, take into account the interactions between particles in solution. GENFIT is able to simultaneously fit more SAS curves via a unique model or a mixture of models. In the latter case, some specific model parameters can be shared by any selection of the experimental curves. Model parameters can be related to the experimental chemical-physical conditions (temperature, pressure, concentration, pH, etc.) by means of link functions, which can be freely defined by the user. On the other hand, GENFIT can be used to generate theoretical SAS curves from a given model and/or from the knowledge of the species in solution. It can hence be a useful instrument to find the optimum experimental conditions for a planned SAS experiment. GENFIT is written in Fortran. Versions 2.0 and higher make use of a graphical user interface (GUI) to manage input files and execute the calculations.

# GNXAS

The GNXAS package is a computer code for EXAFS data analysis based on multiple-scattering (MS) calculations and a rigorous fitting procedure of the raw experimental data. The main characteristic of the software are: + atomic phase shifts calculations in the muffin-tin approximation based on atom self-consistent relativistic calculations. Account for the neighbors is taken. + Inclusion of inelastic losses through complex Hedin-Lundqvist potential. + Calculation of MS signals associated with two, three, and four atom configurations using advanced algorithms. Use of an advanced fitting procedure that allows: + to fit simultaneously any number of spectra containing any number of edges, + to use directly the raw data without any pre-analysis, + to account for complex background multi-electron excitation features, + to use various model peaks for the pair, triplet and quadruplet distribution functions, including non Gaussian models and extreme cases. In all cases absolute parameters can be fitted, - to treat liquid phase or disordered systems and extract reliable g(r) functions in the short range, - to perform a rigorous statistical error analysis and plot two-dimensional correlation maps, - to provide a flexible scientific tool for EXAFS data analysis where the user has access to every stage of the calculation. - full modularity that makes easy to interface parts of the GNXAS software with other available software.

# Grasp

"GRASansP" is a MatlabTM script application designed for the graphical inspection, analysis and reduction of multi-detector data produced by the Small-Angle Neutron Scattering (SANS) instruments of the Institut Laue-Langevin (ILL). GRASansP deals with many of the diverse requirements for analysis and reduction of SANS data using a general set of tools and reduction algorithms. Data from the two ILL SANS instruments, D11 and D22, as well as SANS instruments at some other neutron sources, are currently catered for in the GRASansP package. In principle the architecture and coding of GRASansP combined with the matrix handling abilities, graphics and other advantages of the Matlab™ environment should allow continued development of this software and be able to provide more general aspects of multi-detector and complex data set handling. The drive for producing such a suite of software came from the overwhelming need for a modern, complete and general-purpose package to deal with typical procedures required for analysis of two-dimensional SANS multidetector data. By it’s very nature, two-dimensional data is often best appreciated in a graphical form. The birth of GRASansP came from the need for graphical inspection and ability to be able to quickly process and extract the scattered intensity, I(q), as a function of position on the multidetector (qx,qy) or as a function of sample environment conditions from a series of many measurement runs (e.g. temperature sweep, rocking curve etc.). This, combined with an interest in scientific software development and the abilities of the Matlab™ environment have brought GRASansP into it’s present state.

# GROMACS

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics and energy minimization package mainly designed to simulate the Newtonian equations of motion for systems with hundreds to millions of particles, typically of proteins, lipids and nucleic acids. GROMACS can run on CPUs and GPUs.

# ICSD

Inorganic Crystal Structure Database, containing about 185,000 peer-reviewed data entries of inorganic and related structures, including their atomic coordinates dating back to 1913. It is produced cooperatively by FIZ Karlsruhe and the National Institute of Standards and Technology (NIST).

# idltomo

a graphical user interface to manage tomography data preprocessing, reconstruction and visualizaton based upon IDL and PyHST packages.

# iFit

The iFit library (pronounce [eye-fit]) is a set of methods to load, analyse, plot, fit and optimize models, and export results. iFit is based on Matlab, but can also be launched without Matlab license (stand-alone version).Matlab It does not currently include advanced graphical user interfaces (GUI), and rather focuses on doing the math right. Any text file can be imported straight away, and a set of binary files are supported. Any data dimensionality can be handled, including event based data sets (even though not all methods do work for these). Any model can be assembled for fitting data sets. Last, a number of routines are dedicated to the analyses of S(q,w) and S(alpha,beta). More advanced features include the full automation to compute phonon dispersions in materials, using DFT codes such as ABINIT, ELK, VASP, QuantumEspresso, GPAW and more (Models/sqw_phonons). The software can also compute the neutron TAS resolution function (4D) and fits to experimental data with full resolution convolution (ResLibCal). An interface for McStas and McXtrace is also available to automate and optimize instrument simulations.